Quality assessment for molecular models

Crystallographic Models
About 85% of the molecular models published in the Protein Data Bank come from X-ray crystallography experiments. These crystallographic models vary widely in quality, and rarely they are grossly incorrect. Generally, model quality is indicated by the resolution of the model, the R value, and especially the Free R. Useful information on model quality, including the Ramachandran plots, can be obtained from PDBReports. All-atom contact analysis is a powerful newer method for finding and correcting errors in crystallographic models, made easy and convenient with the MolProbity Server.

Generally, crystallographic models are reliable in most details when they have resolutions of 2.0 Å or better (the lower the number the better), R values of 0.20 or less, and Free R values of 0.25 or less. However, new and important structural insights are often provided by models with much lower resolution. Interestingly, the quality of published molecular models is inversely related to the impacts of the journals in which they are published.

NMR Models
Models resulting from solution NMR experiments account for about 15% of those published in the Protein Data Bank. These are generally less reliable than crystallographic models because the method yields less detailed information. For NMR, there are no widely reported global error estimates equivalent to the crystallographic R value and Free R. Unlike with crystallographic results, it is not possible to distinguish reliable from unreliable NMR models from information included in the PDB files. NMR models are more likely to contain major errors than are crystallographic models that have good Resolution and Free R values.

Global vs. Local Quality
The indicators discussed above, notably resolution, R value, and free R, asses the average or global quality of the model. However, quality and uncertainty are not uniformly distributed throughout the model. Rather, there are regions of higher and lower uncertainty and quality. For crystallographic models, the easiest way to visualize local variations in uncertainty is to color the model by temperature value. As explained in the article on Temperature value, in a temperature-colored model, red atoms have the highest uncertainty in their positions in the model.

For models determined by NMR, disagreement among the ensemble of models in a particular region may signal higher uncertainty, due to local inadequacy of the distance restraints. However, it could also signal thermal motion -- please see NMR Ensembles of Models.

The MolProbity server offers 3D visualization of atomic clashes, with indication of the severity of each clash. The presence of severe clashes indicates greater uncertainty in that local region of the model. MolProbity's analysis, termed all atom contact analysis, can be performed on NMR models (individual models in the ensemble, or the minimized average model) as well as on crystallographic models.

The orientation of the sidechains of Asn, Gln, and His cannot be determined from the electron density in a crystallographic experiment at typical resolution, because of the similarity in electron densities of carbon vs. nitrogen. It is usually straightforward to determine the correct orientation by examining the local environment and optimising hydrogen bonding. Unfortunately, is is common for these determinations not to be made in published crystallographic models. Fortunately, MolProbity does these determinations automatically, and corrects the model by flipping the sidechains of Asn, Gln and HIs when this is warranted.

Improving Published Models
There are several free automated servers that can improve most published models. See Improving published models.

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Portions of this page were adapted from the Glossary of ProteinExplorer.Org, with the permission of the principal author, Eric Martz.